Simon and Elizabeth were always arguing about the upbringing of Emily. Elizabeth wanted to raise her in a protected environment because of her severe genetic condition, but Simon wanted to raise her like any other child.
At many points, Simon thought that he was the direct cause of Emily's hospital stay. He had taken her to an amusement park where she collapsed after falling off a merry-go-round, and he thought he had exposed her to Lyme disease because he had taken her for a walk in the woods.
When Simon found out that Elizabeth had been experimenting on Emily without his knowledge, he tried to remove Emily from the hospital. However, the team talked him out of it.
When Emily's condition was traced to an unrelated atrial myxoma, Simon and Elizabeth started to compromise and agreed to go to the aquarium together with Emily.